uk.ac.ebi.intact.application.dataConversion.psiDownload.UserSessionDownload.createTextNode java code examples

Common ways to obtain UserSessionDownload

private void myMethod () {
 UserSessionDownload u =Conversion.PsiVersion psiVersion;new UserSessionDownload(psiVersion)
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}

/**
 * Create a shortlabel element containing the shortlabel of the given AnnotatatedObject.
 *
 * @param session
 * @param parent  the names element, not null.
 * @param object  the annotatedObject from which we get the shortlabel, not null.
 */
protected void createShortlabel( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  // shortlabel is mandatory in the IntAct API.
  Element shortlabel = session.createElement( "shortLabel" );
  Text shortlabelText = session.createTextNode( object.getShortLabel() );
  shortlabel.appendChild( shortlabelText );
  parent.appendChild( shortlabel );
}

/**
 * Create a shortlabel element containing the shortlabel of the given AnnotatatedObject.
 *
 * @param session
 * @param parent  the names element, not null.
 * @param object  the annotatedObject from which we get the shortlabel, not null.
 */
protected void createShortlabel( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  // shortlabel is mandatory in the IntAct API.
  Element shortlabel = session.createElement( "shortLabel" );
  Text shortlabelText = session.createTextNode( object.getShortLabel() );
  shortlabel.appendChild( shortlabelText );
  parent.appendChild( shortlabel );
}

/**
 * Create a shortlabel element containing the shortlabel of the given AnnotatatedObject.
 *
 * @param session
 * @param parent  the names element, not null.
 * @param object  the annotatedObject from which we get the shortlabel, not null.
 */
protected void createShortlabel( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  // shortlabel is mandatory in the IntAct API.
  Element shortlabel = session.createElement( "shortLabel" );
  Text shortlabelText = session.createTextNode( object.getShortLabel() );
  shortlabel.appendChild( shortlabelText );
  parent.appendChild( shortlabel );
}

Text refText = session.createTextNode( "" + session.getFeatureIdentifier( feature ) );
element.appendChild( refText );

Text refText = session.createTextNode( "" + session.getFeatureIdentifier( feature ) );
element.appendChild( refText );

Text refText = session.createTextNode( "" + session.getFeatureIdentifier( feature ) );
element.appendChild( refText );

private Element createCertainStatus( UserSessionDownload session, Element parent, String tagName ) {
  Element element = session.createElement( tagName );
  // names
  Element nameElement = session.createElement( "names" );
  element.appendChild( nameElement );
  Element shortlabelElement = session.createElement( "shortLabel" );
  nameElement.appendChild( shortlabelElement );
  Text shortlabelTextElement = session.createTextNode( "certain" );
  shortlabelElement.appendChild( shortlabelTextElement );
  // xref
  Element xrefElement = session.createElement( "xref" );
  element.appendChild( xrefElement );
  Element primaryRefElement = session.createElement( "primaryRef" );
  xrefElement.appendChild( primaryRefElement );
  primaryRefElement.setAttribute( "db", CvDatabase.PSI_MI );
  primaryRefElement.setAttribute( "dbAc", CvDatabase.PSI_MI_MI_REF );
  primaryRefElement.setAttribute( "id", "MI:0335" ); // certain, cf. http://psidev.sourceforge.net/mi/rel25/data/psi-mi25.dag
  primaryRefElement.setAttribute( "refType", CvXrefQualifier.IDENTITY );
  primaryRefElement.setAttribute( "refTypeAc", CvXrefQualifier.IDENTITY_MI_REF );
  parent.appendChild( element );
  return element;
}

/**
 * Generates an interactorRef out of an IntAct interactor.
 *
 * @param session
 * @param parent     the Element to which we will add the interactorRef.
 * @param interactor the IntAct interactor that we convert to PSI.
 *
 * @return the generated interactorRef Element.
 */
public Element createInteractorReference( UserSessionDownload session, Element parent, Interactor interactor ) {
  // TODO test that.
  // 1. Checking...
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null UserSessionDownload." );
  }
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null parent to build an " + INTERACTOR_REF_TAG_NAME + "." );
  }
  if ( interactor == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + INTERACTOR_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( INTERACTOR_REF_TAG_NAME );
  Text refText = session.createTextNode( getInteractorId( session, interactor ) );
  element.appendChild( refText );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}

/**
 * Create a fullname element containing the fullname of the given AnnotatatedObject.
 *
 * @param session
 * @param parent  the names element, not null.
 * @param object  the annotatedObject from which we get the fullname, not null.
 */
protected void createFullname( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  // fullname is NOT mandatory in the IntAct API.
  if ( object.getFullName() != null && !"".equals( object.getFullName().trim() ) ) {
    Element fullname = session.createElement( "fullName" );
    Text fullnameText = session.createTextNode( object.getFullName() );
    fullname.appendChild( fullnameText );
    parent.appendChild( fullname );
  }
}

/**
 * Generates an interactorRef out of an IntAct interactor.
 *
 * @param session
 * @param parent     the Element to which we will add the interactorRef.
 * @param interactor the IntAct interactor that we convert to PSI.
 *
 * @return the generated interactorRef Element.
 */
public Element createInteractorReference( UserSessionDownload session, Element parent, Interactor interactor ) {
  // TODO test that.
  // 1. Checking...
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null UserSessionDownload." );
  }
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null parent to build an " + INTERACTOR_REF_TAG_NAME + "." );
  }
  if ( interactor == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + INTERACTOR_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( INTERACTOR_REF_TAG_NAME );
  Text refText = session.createTextNode( getInteractorId( session, interactor ) );
  element.appendChild( refText );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}

/**
 * Create a fullname element containing the fullname of the given AnnotatatedObject.
 *
 * @param session
 * @param parent  the names element, not null.
 * @param object  the annotatedObject from which we get the fullname, not null.
 */
protected void createFullname( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  // fullname is NOT mandatory in the IntAct API.
  if ( object.getFullName() != null && !"".equals( object.getFullName().trim() ) ) {
    Element fullname = session.createElement( "fullName" );
    Text fullnameText = session.createTextNode( object.getFullName() );
    fullname.appendChild( fullnameText );
    parent.appendChild( fullname );
  }
}

/**
 * Generates an interactorRef out of an IntAct interactor.
 *
 * @param session
 * @param parent     the Element to which we will add the interactorRef.
 * @param interactor the IntAct interactor that we convert to PSI.
 *
 * @return the generated interactorRef Element.
 */
public Element createInteractorReference( UserSessionDownload session, Element parent, Interactor interactor ) {
  // TODO test that.
  // 1. Checking...
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null UserSessionDownload." );
  }
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null parent to build an " + INTERACTOR_REF_TAG_NAME + "." );
  }
  if ( interactor == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + INTERACTOR_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( INTERACTOR_REF_TAG_NAME );
  Text refText = session.createTextNode( getInteractorId( session, interactor ) );
  element.appendChild( refText );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}

/**
 * Generated a negative flag if there is one specified annotation in the Interaction or one of its Experiment.
 *
 * @param session     the user session.
 * @param parent      the parent to which we attach the attributeList, and then the attribute.
 * @param interaction the interaction from which we will get the dissociation constant.
 *
 * @return the created flag. May be null.
 *
 * @see uk.ac.ebi.intact.model.Annotation
 * @see uk.ac.ebi.intact.model.Interaction
 * @see uk.ac.ebi.intact.model.Experiment
 */
public Element createNegativeFlag( UserSessionDownload session, Element parent, Interaction interaction ) {
  // TODO test it
  Element element = null;
  if ( isNegative( interaction ) ) {
    element = session.createElement( "negative" );
    Text negativeText = session.createTextNode( "true" );
    // add the text to the node
    element.appendChild( negativeText );
    // add the node to the parent
    parent.appendChild( element );
  }
  return element;
}

/**
 * Create a fullname element containing the fullname of the given AnnotatatedObject.
 *
 * @param session
 * @param parent  the names element, not null.
 * @param object  the annotatedObject from which we get the fullname, not null.
 */
protected void createFullname( UserSessionDownload session, Element parent, AnnotatedObject object ) {
  // fullname is NOT mandatory in the IntAct API.
  if ( object.getFullName() != null && !"".equals( object.getFullName().trim() ) ) {
    Element fullname = session.createElement( "fullName" );
    Text fullnameText = session.createTextNode( object.getFullName() );
    fullname.appendChild( fullnameText );
    parent.appendChild( fullname );
  }
}

private Element createCertainStatus( UserSessionDownload session, Element parent, String tagName ) {
  Element element = session.createElement( tagName );
  // names
  Element nameElement = session.createElement( "names" );
  element.appendChild( nameElement );
  Element shortlabelElement = session.createElement( "shortLabel" );
  nameElement.appendChild( shortlabelElement );
  Text shortlabelTextElement = session.createTextNode( "certain" );
  shortlabelElement.appendChild( shortlabelTextElement );
  // xref
  Element xrefElement = session.createElement( "xref" );
  element.appendChild( xrefElement );
  Element primaryRefElement = session.createElement( "primaryRef" );
  xrefElement.appendChild( primaryRefElement );
  primaryRefElement.setAttribute( "db", CvDatabase.PSI_MI );
  primaryRefElement.setAttribute( "dbAc", CvDatabase.PSI_MI_MI_REF );
  primaryRefElement.setAttribute( "id", "MI:0335" ); // certain, cf. http://psidev.sourceforge.net/mi/rel25/data/psi-mi25.dag
  primaryRefElement.setAttribute( "refType", CvXrefQualifier.IDENTITY );
  primaryRefElement.setAttribute( "refTypeAc", CvXrefQualifier.IDENTITY_MI_REF );
  parent.appendChild( element );
  return element;
}

private Element createCertainStatus( UserSessionDownload session, Element parent, String tagName ) {
  Element element = session.createElement( tagName );
  // names
  Element nameElement = session.createElement( "names" );
  element.appendChild( nameElement );
  Element shortlabelElement = session.createElement( "shortLabel" );
  nameElement.appendChild( shortlabelElement );
  Text shortlabelTextElement = session.createTextNode( "certain" );
  shortlabelElement.appendChild( shortlabelTextElement );
  // xref
  Element xrefElement = session.createElement( "xref" );
  element.appendChild( xrefElement );
  Element primaryRefElement = session.createElement( "primaryRef" );
  xrefElement.appendChild( primaryRefElement );
  primaryRefElement.setAttribute( "db", CvDatabase.PSI_MI );
  primaryRefElement.setAttribute( "dbAc", CvDatabase.PSI_MI_MI_REF );
  primaryRefElement.setAttribute( "id", "MI:0335" ); // certain, cf. http://psidev.sourceforge.net/mi/rel25/data/psi-mi25.dag
  primaryRefElement.setAttribute( "refType", CvXrefQualifier.IDENTITY );
  primaryRefElement.setAttribute( "refTypeAc", CvXrefQualifier.IDENTITY_MI_REF );
  parent.appendChild( element );
  return element;
}

/**
 * Generated a negative flag if there is one specified annotation in the Interaction or one of its Experiment.
 *
 * @param session     the user session.
 * @param parent      the parent to which we attach the attributeList, and then the attribute.
 * @param interaction the interaction from which we will get the dissociation constant.
 *
 * @return the created flag. May be null.
 *
 * @see uk.ac.ebi.intact.model.Annotation
 * @see uk.ac.ebi.intact.model.Interaction
 * @see uk.ac.ebi.intact.model.Experiment
 */
public Element createNegativeFlag( UserSessionDownload session, Element parent, Interaction interaction ) {
  // TODO test it
  Element element = null;
  if ( isNegative( interaction ) ) {
    element = session.createElement( "negative" );
    Text negativeText = session.createTextNode( "true" );
    // add the text to the node
    element.appendChild( negativeText );
    // add the node to the parent
    parent.appendChild( element );
  }
  return element;
}

/**
 * Generated a negative flag if there is one specified annotation in the Interaction or one of its Experiment.
 *
 * @param session     the user session.
 * @param parent      the parent to which we attach the attributeList, and then the attribute.
 * @param interaction the interaction from which we will get the dissociation constant.
 *
 * @return the created flag. May be null.
 *
 * @see uk.ac.ebi.intact.model.Annotation
 * @see uk.ac.ebi.intact.model.Interaction
 * @see uk.ac.ebi.intact.model.Experiment
 */
public Element createNegativeFlag( UserSessionDownload session, Element parent, Interaction interaction ) {
  // TODO test it
  Element element = null;
  if ( isNegative( interaction ) ) {
    element = session.createElement( "negative" );
    Text negativeText = session.createTextNode( "true" );
    // add the text to the node
    element.appendChild( negativeText );
    // add the node to the parent
    parent.appendChild( element );
  }
  return element;
}

  private Element createConfidenceElement(UserSessionDownload session, CvObject unit, Object value) {
    Element confidenceElement = session.createElement(CONFIDENCE_TAG_NAME);

    // 2. Generating Unit...
    Element unitElement = session.createElement(CONFIDENCE_UNIT_TAG_NAME);
    createNames(session, unitElement, unit);
    confidenceElement.appendChild(unitElement);

    // TODO check if it has MI reference, if so export them as xref of the confidence.unit.

    // 3. Generating value...
    Element valueElement = session.createElement(CONFIDENCE_VALUE_TAG_NAME);
    Text valueTextElement = session.createTextNode((String)value);
    valueElement.appendChild(valueTextElement);
    confidenceElement.appendChild(valueElement);
    return confidenceElement;
  }
}

Text refText = session.createTextNode( getExperimentId( session, experiment ) );
element.appendChild( refText );

Popular methods of UserSessionDownload

<init>
addMessage
createElement
declareAlreadyDefined
Declare in the session that the given protein has been already converted in XML.
filterObsoleteAnnotationTopic
Load all CvTopic and check which one have been flagged 'obsolete'. Those CvTopic are automatically a
getAvailabilityListElement
Return the availabilityList element under the entry of the PSI document. If the element doesn't exis
getCvObjectCache
getEntryElement
Return the entry element of the PSI document. If the element doesn't exist, it is created.
getExperimentIdentifier
Get a specific identifier for the given experiemnt. If an identifier had already been affected for t
getExperimentListElement
Return the experimentList element under the entry of the PSI document. If the element doesn't exist,
getFeatureIdentifier
Get a specific identifier for the given feature. If an identifier had already been affected for that
getHostOrganismCache

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How to use createTextNodemethodin uk.ac.ebi.intact.application.dataConversion.psiDownload.UserSessionDownload

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uk.ac.ebi.intact.application.dataConversion.psiDownload.UserSessionDownload